Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution inUrochloa(Brachiaria) species

Abstract

Background and Aims: Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods: Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes. Key Results: Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions: We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

“…The average DNA content and genome sizes given as Cx values have been published already for Urochloa species [ 27 , 63 ]. Most diploid accessions of U. brizantha studied here are apomict [ 9 ], showing larger fluorescence values of the peak positions than sexual diploid accessions of U. decumbens and U. ruziziensis , proving that the genome size depends on the mode of reproduction [ 63 ], which is an additional challenge for screening diverse germplasm collections. While in diploid and polyploid accessions of U. decumbens a small shift in peak position on histogram usually does not compromise reliability of ploidy estimates, attention should be paid to the analysis of U. brizantha showing odd ploidy levels, because relative differences in fluorescence values of the peak positions between neighboring cytotypes (2 x , 4 x , 5 x , 6 x ) is decreased; such a phenomenon is also observed in species with ploidy levels greater than 6x [ 44 ].…”

“…Some of them are included in the current breeding programs at CIAT and EMBRAPA, now mainly focused on crossing tetraploids within ‘ brizantha ’ and ‘ humidicola ’ agamic complexes and Urochloa maxima [ 65 ], but other species studied here can also be included and used as fodder plants. This tropical forage grass group is genomically complex [ 9 ], having species recognized as being very variable in number of chromosomes, and ploidy levels which is the result of apomictic reproduction, and reflecting the genetic diversity present in a given population [ 66 ]. The ploidy levels of some Urochloa accessions have been previously measured [ 25 , 65 , 67 , 68 , 69 ], but some data vary between papers and reports [ 9 ]: thus, values may require checking for a particular accession name.…”

“…This tropical forage grass group is genomically complex [ 9 ], having species recognized as being very variable in number of chromosomes, and ploidy levels which is the result of apomictic reproduction, and reflecting the genetic diversity present in a given population [ 66 ]. The ploidy levels of some Urochloa accessions have been previously measured [ 25 , 65 , 67 , 68 , 69 ], but some data vary between papers and reports [ 9 ]: thus, values may require checking for a particular accession name.…”

“…By introduction to plant breeding programmes, genetic improvement of forage lines, recurrent genetic selection of plants showing useful traits, and subsequent hybridizations and back-crossings [ 5 , 6 ], create more diverse agroecosystems resilient to climate and environmental changes [ 7 ]. The DNA amount measurement for ploidy and genome size estimation, and the characterization of genome composition are required for effective use of diploids and polyploids in breeding programs, as well as for research purposes [ 8 , 9 ].…”

“…For Urochloa , ploidy estimation across the whole germplasm collection (excluding one species, U. ruziziensis , known only as a diploid) is required due to the different pathways of reproduction showing sexual and apomictic accessions within same species [ 26 ], natural triploid interspecific hybrids [ 27 ], different genome compositions both within and between species [ 9 ], confirmed aneuploidy [ 9 , 28 , 29 ], and different basic chromosome numbers ( x = 6, 8 and 9) [ 30 , 31 , 32 , 33 , 34 , 35 ].…”